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1.  PICH and BLM limit histone association with anaphase centromeric DNA threads and promote their resolution 
The EMBO Journal  2011;30(16):3309-3321.
PICH and BLM limit histone association with anaphase centromeric DNA threads and promote their resolution
The helicase proteins PICH and BLM localize to ultrafine DNA threads between separating sister chromatids. It now appears they cooperate to remove histones from these anaphase DNA bridges, to allow their stretching and unravelling without breakage.
Centromeres nucleate the formation of kinetochores and are vital for chromosome segregation during mitosis. The SNF2 family helicase PICH (Plk1-interacting checkpoint helicase) and the BLM (the Bloom's syndrome protein) helicase decorate ultrafine histone-negative DNA threads that link the segregating sister centromeres during anaphase. The functions of PICH and BLM at these threads are not understood, however. Here, we show that PICH binds to BLM and enables BLM localization to anaphase centromeric threads. PICH- or BLM-RNAi cells fail to resolve these threads in anaphase. The fragmented threads form centromeric-chromatin-containing micronuclei in daughter cells. Anaphase threads in PICH- and BLM-RNAi cells contain histones and centromere markers. Recombinant purified PICH has nucleosome remodelling activities in vitro. We propose that PICH and BLM unravel centromeric chromatin and keep anaphase DNA threads mostly free of nucleosomes, thus allowing these threads to span long distances between rapidly segregating centromeres without breakage and providing a spatiotemporal window for their resolution.
PMCID: PMC3160651  PMID: 21743438
centromere; chromatin remodelling; DNA repair; mitosis
2.  On an Additive Semigraphoid Model for Statistical Networks With Application to Pathway Analysis 
We introduce a nonparametric method for estimating non-gaussian graphical models based on a new statistical relation called additive conditional independence, which is a three-way relation among random vectors that resembles the logical structure of conditional independence. Additive conditional independence allows us to use one-dimensional kernel regardless of the dimension of the graph, which not only avoids the curse of dimensionality but also simplifies computation. It also gives rise to a parallel structure to the gaussian graphical model that replaces the precision matrix by an additive precision operator. The estimators derived from additive conditional independence cover the recently introduced nonparanormal graphical model as a special case, but outperform it when the gaussian copula assumption is violated. We compare the new method with existing ones by simulations and in genetic pathway analysis.
PMCID: PMC4577248  PMID: 26401064
Additive conditional independence; additive precision operator; copula; conditional independence; covariance operator; gaussian graphical model; nonparanormal graphical model; reproducing kernel Hilbert space
3.  Sparse Semiparametric Nonlinear Model with Application to Chromatographic Fingerprints 
Traditional Chinese herbal medications (TCHMs) are comprised of a multitude of compounds and the identification of their active composition is an important area of research. Chromatography provides a visual representation of a TCHM sample's composition by outputting a curve characterized by spikes corresponding to compounds in the sample. Across different experimental conditions, the location of the spikes can be shifted, preventing direct comparison of curves and forcing compound identification to be possible only within each experiment. In this article we propose a sparse semiparametric nonlinear modeling framework for the establishment of a standardized chromatographic fingerprint. Data-driven basis expansion is used to model the common shape of the curves while a parametric time warping function registers across individual curves. Penalized weighted least squares with the adaptive lasso penalty provides a unified criterion for registration, model selection, and estimation. Furthermore, the adaptive lasso estimators possess attractive sampling properties. A back-fitting algorithm is proposed for estimation. Performance is assessed through simulation and we apply the model to chromatographic data of rhubarb collected from different experimental conditions and establish a standardized fingerprint as a first step in TCHM research.
PMCID: PMC4574961  PMID: 26388659
Adaptive lasso; Chromatography; Curve registration; Herbal medicine; Variable selection
4.  Increasing proline and myo-inositol improves tolerance of Saccharomyces cerevisiae to the mixture of multiple lignocellulose-derived inhibitors 
The development of robust microbes with tolerance to the combined lignocellulose-derived inhibitors is critical for the efficient cellulosic ethanol production. However, the lack of understanding on the inhibition mechanism limited the rational engineering of tolerant strain. Here, through the metabolomic analysis of an adaptation process of Saccharomyces cerevisiae to representative inhibitors, i.e., furfural, acetic acid and phenol (FAP), we figured out the new candidates for improving inhibitor tolerance.
After metabolomic analysis, proline and myo-inositol were identified as the potential metabolites responsible for strain tolerance to inhibitors. The deletion of genes involved in proline or myo-inositol synthesis weakened strain tolerance against FAP stress. On the contrary, the addition of proline or myo-inositol in medium exerted a protective effect on cell growth under FAP stress. Furthermore, the enhancement of proline or myo-inositol synthesis by overexpressing key gene PRO1 or INO1 conferred yeast strain significantly increased FAP tolerance. All the recombinant strains finished the fermentation within 60 h under FAP stress, while the control strain was still in the lag phase. Meanwhile, it was found that the intracellular level of reactive oxygen species (ROS) under FAP condition was decreased with the increase of proline content, suggesting the function of proline as a ROS scavenger to protect strains from inhibitor damage.
Increasing proline and myo-inositol were uncovered as the new determinants for improving strain tolerance to FAP under the guidance of metabolomics. Meanwhile, this study displayed the powerful application of metabolomics to develop rational strategies to increase stress tolerance and provided valuable insights into the design of recombinant microbes for the complex traits.
Electronic supplementary material
The online version of this article (doi:10.1186/s13068-015-0329-5) contains supplementary material, which is available to authorized users.
PMCID: PMC4570682  PMID: 26379774
Synthetic biology; Metabolomics; Tolerance; Lignocellulose-derived inhibitors; Proline; Myo-inositol
5.  Potential Renoprotective Agents through Inhibiting CTGF/CCN2 in Diabetic Nephropathy 
Journal of Diabetes Research  2015;2015:962383.
Diabetic nephropathy (DN) is the leading cause of end-stage renal disease (ESRD). The development and progression of DN might involve multiple factors. Connective tissue growth factor (CCN2, originally known as CTGF) is the one which plays a pivotal role. Therefore, increasing attention is being paid to CCN2 as a potential therapeutic target for DN. Up to date, there are also many drugs or agents which have been shown for their protective effects against DN via different mechanisms. In this review, we only focus on the potential renoprotective therapeutic agents which can specifically abolish CCN2 expression or nonspecifically inhibit CCN2 expression for retarding the development and progression of DN.
PMCID: PMC4572424  PMID: 26421309
6.  Opsismodysplasia resulting from an insertion mutation in the SH2 domain which destabilizes INPPL1 
PMCID: PMC4134718  PMID: 24953221
Opsismodysplasia; INPPL1; Skeletal dysplasia; Cartilage; Chondrodysplasia
7.  CYP2E1 Rsa Ι/Pst Ι polymorphism and lung cancer susceptibility: a meta-analysis involving 10,947 subjects 
Many studies have examined the association between the CYP2E1 Rsa Ι/Pst Ι (rs3813867) polymorphism gene polymorphisms and lung cancer risk in various populations, but their results have been inconsistent. The PubMed and CNKI database was searched for case–control studies published up to October 2013. Data were extracted and pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated. In this meta-analysis, we assessed 23 published studies involving comprising 4727 lung cancer cases and 6220 controls of the association between CYP2E1 Rsa Ι/Pst Ι polymorphism and lung cancer risk. For the homozygote c2/c2 and c2 allele carriers (c1/c2 + c2/c2), the pooled ORs for all studies were 0.73(95% CI = 0.62–0.84; P = 0.005 for heterogeneity) and 0.84 (95% CI = 0.77–0.92; P = 0.001 for heterogeneity) when compared with the homozygous wild-type genotype (c1/c1). In the stratified analysis by ethnicity, the same significantly risks were found among Asians and mixed population for both the c2 allele carriers and homozygote c2/c2. However, no significant associations were found in Caucasian population all genetic models. This updated meta-analysis suggests that CYP2E1 Rsa Ι/Pst Ι c2 allele is a decreased risk factor for the developing lung cancer among Asians and mixed population.
PMCID: PMC4568918  PMID: 25945422
CYP2E1; polymorphism; lung cancer; susceptibility; meta-analysis
8.  Photo-thermal effect enhances the efficiency of radiotherapy using Arg-Gly-Asp peptides-conjugated gold nanorods that target αvβ3 in melanoma cancer cells 
Thermotherapy has been known to be one of the most effective adjuvants to radiotherapy (RT) in cancer treatment, but it is not widely implemented clinically due to some limitations, such as, inadequate temperature concentrations to the tumor tissue, nonspecific and non-uniform distribution of heat. So we constructed arginine-glycine-aspartate peptides-conjugated gold nanorods (RGD-GNRs) that target the alpha(v) beta(3) Integrin (αvβ3) and investigate whether the photo-thermal effect of RGD-GNRs by near infrared radiation (NIR) could enhance the efficiency of RT in melanoma cancer cells.
RGD-GNRs could be seen both on the surface of the cell membranes and cytoplasm of A375 cells with high expression of αvβ3. After exposed to 808 nm NIR, RGD-GNRs with various concentrations could be rapidly heated up. Compared to other treatments, flow cytometric analysis indicated that RT + NIR + RGD-GNRs increased apoptosis (p < 0.001) and decreased the proportion of cells in the more radioresistant S phase (p = 0.014). Treated with NIR + RGD-GNRs, the radiosensitivity was also significantly enhanced (DMFSF2: 1.41).
Results of the current study showed the feasibility of using RGD-GNRs for synergetic RT with photo-thermal therapy. And it would greatly benefit the therapeutic effects of refractory or recurrent malignant cancers.
PMCID: PMC4552250  PMID: 26315288
Arg-Gly-Asp peptides; Gold nanorods; Integrin αvβ3; Photo-thermal therapy; Radiotherapy
9.  Stabilization of 4H hexagonal phase in gold nanoribbons 
Nature Communications  2015;6:7684.
Gold, silver, platinum and palladium typically crystallize with the face-centred cubic structure. Here we report the high-yield solution synthesis of gold nanoribbons in the 4H hexagonal polytype, a previously unreported metastable phase of gold. These gold nanoribbons undergo a phase transition from the original 4H hexagonal to face-centred cubic structure on ligand exchange under ambient conditions. Using monochromated electron energy-loss spectroscopy, the strong infrared plasmon absorption of single 4H gold nanoribbons is observed. Furthermore, the 4H hexagonal phases of silver, palladium and platinum can be readily stabilized through direct epitaxial growth of these metals on the 4H gold nanoribbon surface. Our findings may open up new strategies for the crystal phase-controlled synthesis of advanced noble metal nanomaterials.
Noble metals typically crystallize with the face-centered cubic structure. Here, the authors report the synthesis of gold nanoribbons in the 4H hexagonal polytype, a previously unreported, metastable phase of gold, and use it to stabilize 4H hexagonal phases of silver, palladium and platinum.
PMCID: PMC4525209  PMID: 26216712
10.  Operative versus nonoperative treatment for displaced midshaft clavicle fractures: a meta-analysis based on current evidence 
Clinics  2015;70(8):584-592.
Literature searches of the Cochrane Library, PubMed, EMBASE, Web of Science, LILACS, China National Knowledge Infrastructure, and Wanfang Data databases were performed from 1966 to September 2014. Only randomized and quasi-randomized controlled clinical trials comparing operative and nonoperative treatments for displaced midshaft clavicle fractures were included. Data collection and extraction, quality assessment, and data analyses were performed according to the Cochrane standards. Thirteen studies were considered in the meta-analysis. Constant scores and the Disabilities of the Arm, Shoulder and Hand scores were improved in the operative fixation group at a follow up of one year or more. The nonunion and symptomatic malunion rates were significantly lower in the operative group. Additionally, the nonoperative group had a higher likelihood of neurological symptoms compared with the operative group. A significantly higher risk of complications was found in patients treated conservatively than in those who underwent operative fixation. However, when patients with nonunion and symptomatic malunion were excluded from the analysis, no significant differences in the complication rate were found. We concluded that based on the current clinical reports, operative treatment is superior to nonoperative treatment in the management of displaced midshaft clavicle fractures. However, we do not support the routine use of primary operative fixation for all displaced midshaft clavicle fractures in adults.
PMCID: PMC4518819  PMID: 26247672
Clavicle; Midshaft clavicles; Operative treatment; Nonoperative treatment; Meta-analysis
11.  Expression of EGFR Is Closely Related to Reduced 3-Year Survival Rate in Chinese Female NSCLC 
Non-small cell lung cancer (NSCLC) accounts for approximately 80% of lung carcinoma cases, which becomes more and more important in the field of lung carcinoma as well as primary lung carcinoma in females.
We analyzed the medical history of 62 female NSCLC patients. Immunohistochemistry was used to observe and compare the expression of EGFR. The chi-square test was conducted to analyze associations between EGFR expression and the different variables. The cumulative survival rate was determined by the Kaplan-Meier product-limit method. The prognosis of female patients with NSCLC was examined by using a multivariate Cox proportional hazard regression model.
The expression proportion of EGFR in Chinese female NSCLC patients was 70.97%, and it was remarkably higher in adenocarcinoma than in squamous cell carcinoma and bronchioloalveolar carcinoma. A positive correlation was observed between EGFR expression and tumor-node metastasis staging or lymph node metastasis. The Cox proportional risk model analysis showed a correlation between postoperative survival time of the patients and pathology of the tumor type and lymph node metastasis.
Expression of EGFR was closely related to pathology of the tumor type, tumor-node metastasis staging, and lymph node metastasis, which could be used as a promising indicator of NSCLC in Chinese female patients.
PMCID: PMC4554359  PMID: 26230859
Carcinoma, Non-Small-Cell Lung; Female; Immunohistochemistry; Receptors, Vascular Endothelial Growth Factor
12.  Effects of ketamine exposure on dopamine concentrations and dopamine type 2 receptor mRNA expression in rat brain tissue 
Objective: To explore the effects of ketamine abuse on the concentration of dopamine (DA), a monoamine neurotransmitter, and the mRNA expression of dopamine type 2 (D2) receptors in brain tissue, we used male Wistar rats to model ketamine abuse through chronic intraperitoneal infusion of ketamine across different doses. Methods: The rats were sacrificed 45 minutes and 1, 2, and 3 weeks after initiating the administration of ketamine or normal saline, as well as 3 days following discontinuation. Brain tissue was harvested to examine the concentration of 2,5-dihydroxyphenylacetic acid and homovanillic acid, the primary metabolites of DA, as well as the expression of D2 receptor mRNA. In addition, behavioral changes were observed within 30 minutes of administration, and withdrawal symptoms were also documented. A factorial experimental design was used to investigate variations and correlations in the primary outcome measures across the four doses and five time points. Brain DA concentrations were significantly higher in the ketamine-treated groups compared with the saline-treated group, with 30 mg/kg > 10 mg/kg > 60 mg/kg > saline (P < 0.05). The D2 receptor mRNA expression exhibited an inverse downregulation pattern, with 30 mg/kg < 10 mg/kg < 60 mg/kg < saline (P < 0.05). In the 10 mg/kg and 30 mg/kg ketamine-treated groups, the DA concentration and D2 receptor mRNA level in the brain tissue correlated with the dose of ketamine (r = 0.752, r = -0.806), but no significant correlation was found in the 60 mg/kg group. Result: These findings indicated that chronic dosing with ketamine increased the concentration of DA in rat brain tissue by increasing DA release or interrupting DA degradation. D2 receptor mRNA expression likely decreased because of stimulation with excessive DA. Conclusion: High-dose (60 mg/kg) ketamine had potent paralyzing effects on the central nervous system of rats and weakened the excitatory effects of the limbic system. Brain DA and D2 receptor mRNA may be associated with ketamine abuse.
PMCID: PMC4565304  PMID: 26379921
Ketamine; rat brain; dopamine; dopamine type 2 receptor mRNA; abuse
13.  TP53 codon 72 polymorphism and susceptibility to cervical cancer in the Chinese population: an update meta-analysis 
Background: Although many epidemiologic studies investigated the TP53 codon 72 polymorphism and its association with cervical cancer (CC), definite conclusions cannot be drawn. Aim of the study: To evaluate the association between TP53 codon 72 polymorphism and risk of cervical cancer in the Chinese population. Methods: A computerized literature search was carried out in PubMed, Springer Link, Ovid, Chinese Biomedical Database (CBM), Chinese National Knowledge Infrastructure (CNKI), and Chinese Wanfang Database to collect relevant articles. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to calculate the strength of association. Results: A total of 16 studies including 1684 CC cases and 1178 controls were involved in this meta-analysis. Overall, significant increased association was found between the Pro/Pro carriers and CC risk when all studies in Chinese population pooled into the meta-analysis (heterozygous model: OR = 1.22, 95% CI: 1.01-1.46). In subgroup analyses stratified by ethnicity and source of controls, the same results were observed in Han and in hospital-based studies. Conclusion: Our results suggest that the TP53 codon 72 polymorphism may be potential biomarkers for CC risk in the Chinese population, especially for Han Chinese, and studies with wider spectrum of population are required for definite conclusions.
PMCID: PMC4538048  PMID: 26309559
Meta-analysis; TP53; Codon 72; polymorphism; cervical cancer
14.  Fatty acid binding protein E-FABP restricts tumor growth by promoting IFNβ responses in tumor-associated macrophages 
Cancer research  2014;74(11):2986-2998.
Fatty acid binding proteins (FABPs) are known central regulators of both metabolic and inflammatory pathways, but their role in tumor development remains largely unexplored. Here, we report that host expression of epidermal FABP (E-FABP) protects against mammary tumor growth. We find that E-FABP is highly expressed in macrophages, particularly in a specific subset, promoting their antitumor activity. In the tumor stroma E-FABP-expressing tumor-associated macrophages (TAMs) produce high levels of interferon β (IFNβ) through upregulation of lipid droplet (LD) formation in response to tumors. E-FABP-mediated IFNβ signaling can further enhance recruitment of tumoricidal effector cells, in particular NK cells, to the tumor stroma for antitumor activity. These findings identify E-FABP as a new protective factor to strengthen IFNβ responses against tumor growth.
PMCID: PMC4040301  PMID: 24713431
15.  A Rapid Method to Achieve Aero-Engine Blade Form Detection 
Sensors (Basel, Switzerland)  2015;15(6):12782-12801.
This paper proposes a rapid method to detect aero-engine blade form, according to the characteristics of an aero-engine blade surface. This method first deduces an inclination error model in free-form surface measurements based on the non-contact laser triangulation principle. Then a four-coordinate measuring system was independently developed, a special fixture was designed according to the blade shape features, and a fast measurement of the blade features path was planned. Finally, by using the inclination error model for correction of acquired data, the measurement error that was caused by tilt form is compensated. As a result the measurement accuracy of the Laser Displacement Sensor was less than 10 μm. After the experimental verification, this method makes full use of optical non-contact measurement fast speed, high precision and wide measuring range of features. Using a standard gauge block as a measurement reference, the coordinate system conversion data is simple and practical. It not only improves the measurement accuracy of the blade surface, but also its measurement efficiency. Therefore, this method increases the value of the measurement of complex surfaces.
PMCID: PMC4507604  PMID: 26039420
blade; laser displacement sensor; freeform surface; error compensation; four-coordinate measuring system
16.  Decreased expression of miR-378 correlates with tumor invasiveness and poor prognosis of patients with glioma 
microRNAs (miRNAs) are a class of small non-coding RNAs that play important roles in a variety of biological process. It has been reported that dysregulation of miRNA is always associated with cancer progression and development, and miR-378 aberrant expression has been found in some types of cancers. However, the association of miR-378 and glioma has not been evaluated. In this work, we measured the expression of miR-378 in glioma tissues and non-neoplastic brain tissues was measured using real-time PCR, and found that miRNA-378 expression level was significantly lower in glioma tissues compared with non-neoplastic brain tissues. Patients with lower miR-378 expression level had significantly poorer overall survival. Multivariate Cox regression analysis showed that miR-378 expression was an independent prognostic factor for 5-year overall survival. Over-expression of miR-378 inhibits glioma cell migration and invasion. In conclusion, our results indicated that miR-378 may serve as a tumor suppressor and play an important role in inhibiting tumor migration and invasion. Our work implicates the potential effect of miR-378 on the prognosis of glioma.
PMCID: PMC4525926  PMID: 26261592
miR-378; glioma; prognosis; cell migration and invasion
17.  Expression of SIRT1 and oxidative stress in diabetic dry eye 
Objective: To explore the expression of SIRT1 with oxidative stress and observe physiological and pathological changes in the corneas as well as the association between SIRT1 and oxidative stress of diabetic dry eyes in mice. Method: Forty-eight C57BL/6Jdb/db mice at eight weeks of age were divided randomly into two groups: the diabetic dry eye group and the diabetic group. An additional forty-eight C57BL/6J mice at eight weeks of age were divided randomly into two groups: the dry eye group and the control group. Every mouse in the dry eye groups (diabetic and normal) was injected with scopolamine hydrobromide three times daily, combined with low humidity to establish a dry eye model. After the intervention, phenol red cotton string tests and corneal fluorescein staining were performed. In addition, HE staining and immunofluorescence were done. Expression of SIRT1 in the cornea was examined by real-time PCR and Western Blot and expression of FOXO3 and MnSOD proteins was detected by Western Blot. Results: At one, four, and eight weeks post intervention, all of the groups except the controls showed significant decreases in tear production and increases in the corneal fluorescein stain (P<0.05 vs control). Between the experimental groups, the diabetic dry eye group had the least tear production and the highest corneal fluorescein stain score (P<0.05). As the disease progressed, all of the experimental groups showed obviously pathological changes in HE staining, particularly the diabetic dry eye group. In the 1st and 4th week, the expression of SIRT1, FOXO3, and MnSOD were significantly higher in the diabetic DE and DM groups but lower in the DE group compared to the controls (P<0.05). In the 8th week, the expression of SIRT1, FOXO3, and MnSOD was significantly down-regulated in the diabetic DE group and the DM group (P<0.05). Immunofluorescence showed similar results. Conclusion: In the condition of diabetic dry eye, tear production declined markedly coupled with seriously wounded corneal epithelium. Oxidative stress in the cornea was enhanced significantly and the expression of SIRT1 was decreased.
PMCID: PMC4526019  PMID: 26261685
Dry eye; diabetes mellitus; SIRT1; FOXO3; MnSOD; cornea
18.  Serum iron metabolism and erythropoiesis in patients with myelodysplastic syndrome not receiving RBC transfusions 
Leukemia research  2014;38(5):545-550.
Dysregulation of hepcidin, a key iron regulating hormone, is important in the pathogenesis of iron overload in patients with myelodysplatic syndrome (MDS). However, most studies of hepcidin levels are complicated by concomitant RBC transfusions. To evaluate the relationship between iron metabolism and erythropoiesis, we measured serum levels of hepcidin, growth-differentiation factor-15 (GDF15) and other markers of erythropoiesis in 107 subjects with MDS not receiving RBC transfusions. Patients with MDS had significantly higher levels of hepcidin than normals. However, their hepcidin–ferritin ratio was markedly decreased compared to normals (P < 0.001) and varied substantially between MDS subtypes (P = 0.011). GDF15 levels positively correlated with percent of bone marrow erythroblasts (P < 0.001), soluble transferrin receptor (sTfR) (P = 0.018), and also with transferrin saturation (ISAT) (P = 0.038). The hepcidin–ferritin ratio negatively correlated with serum erythropoietin (EPO) levels (P < 0.001), and also with GDF15 levels (P = 0.014). Colony forming cells (CFC) were evaluated in 70 subjects. Those with serum ferritin (SF) levels <500 ng/ml had significantly more BFU-E than subjects with SF≥ 500 ng/L (P = 0.007), but numbers of granulocyte/macrophage-colony-forming cells (CFU-GM) were similar (P = 0.190). Our data indicate serum hepcidin levels are inappropriately low in patients MDS not receiving RBC transfusions. GDF15 levels correlated with low hepcidin levels and may contribute to iron overload in this setting. Iron overload may in turn suppress erythropoiesis by imparing the proliferative capacity of the erythroid progenitor cells.
PMCID: PMC4439195  PMID: 24598841
Myelodysplastic syndromes; Iron metabolism; Hematopoiesis
19.  Impact of TET2, SRSF2, ASXL1 and SETBP1 mutations on survival of patients with chronic myelomonocytic leukemia 
Chronic myelomonocytic leukemia (CMML) is a myeloid neoplasm classified in the myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN) category. Molecular abnormalities are reported in about 90 % of patients with CMML. ASXL1 and SETBP1 mutations, but not TET2 or SFRS2 mutations are reported to be associated with prognosis.
We studied frequency of TET2, SRSF2, ASXL1 and SETBP1 mutations in 145 patients with CMML using Sanger sequencing, and determined the prognostic factors for OS. We also identified the predictive value of ASXL1 mutations (frameshift and nonsense mutations) through comparing the Mayo Prognostic Model with the Mayo Molecular Model.
Forty-seven (32 %) had a mutation in TET2, 42 (29 %), a mutation in SRSF2, 65 (45 %), a mutation (nonsense and frame-shift) in ASXL1 and 26 (18 %), a mutation in SETBP1. Significant variables in multivariable analysis of survival included ASXL1 (HR = 1.99 [1.20–3.28]; P = 0.007), hemoglobin <100 g/L (HR = 2.42 [1.40–4.19]; P = 0.002) and blood immature myeloid cells (IMCs) (HR = 2.08 [1.25–3.46]; P = 0.005). When our patients were analyzed using the Mayo Prognostic Model median OS were not reached, 26 months and 15 months (P = 0.014). An analysis using the Mayo Molecular Model identified 4 cohorts with median OS of not reached, 70 months, 26 months and 11 months (P < 0.001). Data fitting using our patients suggest the Molecular Mayo Model has significantly higher survival predictive power compared with Mayo Prognostic Model (P < 0.001, −2 log-likelihood ratios of 538.070 and 552.260).
There were high frequencies of mutations in TET2, SRSF2, ASXL1 and SETBP1 in patients with CMML. With the addition of ASXL1 frameshift and nonsense mutations, the Mayo Molecular Model fitted better than Mayo Prognostic Model of our patients.
PMCID: PMC4445804  PMID: 26019984
Chronic myelomonocytic leukemia; Mutation; Prognostic model
20.  Circulating microRNAs in esophageal squamous cell carcinoma: association with locoregional staging and survival 
Locoregional staging and prognostic information play a critical role in esophageal squamous cell carcinoma (ESCC) treatment strategies. Although microRNA (miRNA) is a promising marker for cancer detection, the relationship between circulating plasma miRNAs and ESCC remains unclear. Our study aims to investigate the association between circulating plasma miRNAs and tumor diagnosis or prognosis in ESCC patients. Plasma levels of miR-16, miR-21, miR-22, miR-126, miR-148b, miR-185, miR-221, miR-223, and miR-375 were evaluated by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assays from 38 ESCC patients prior to treatment and 19 healthy subjects. Differences in selected miRNAs and their diagnostic and prognostic value were examined. Levels of four of the selected miRNAs were found to be significantly higher in ESCC patients than in controls; namely, miR-16, miR-21, miR-185, and miR-375 (P < 0.050). In addition, the area under the receiver operating characteristic (ROC) curve (AUC) for miR-375 was 0.921 (95% confidence interval [CI] 0.817-0.976). Moreover, the expression levels of miR-16 were higher in patients with T3-4 tumors than in patients with T1-2 tumors (P = 0.020). Kaplan-Meier survival analysis showed that high expression levels of miR-16 and miR-21 in the plasma correlated significantly with shortened progression-free survival (PFS; P = 0.031 and P = 0.038, respectively) and overall survival (OS; P = 0.022 and P = 0.041, respectively) in ESCC patients. Four plasma miRNAs were identified that could potentially serve as novel diagnostic biomarkers for ESCC. Moreover, specific miRNAs, such as miR-16 and miR-21, can predict poor survival in ESCC.
PMCID: PMC4509208  PMID: 26221263
MicroRNA; esophageal squamous cell carcinoma; locoregional staging; prognosis
21.  Targeting epidermal fatty acid binding protein for treatment of experimental autoimmune encephalomyelitis 
BMC Immunology  2015;16:28.
Multiple sclerosis (MS) is an autoimmune disease in which dysregulated immune cells attack myelin in the central nervous system (CNS), leading to irreversible neuronal degeneration. Our previous studies have demonstrated that epidermal fatty acid binding protein (E-FABP), widely expressed in immune cells, in particular in dendritic cells (DCs) and T lymphocytes, fuels the overactive immune responses in the mouse model of experimental autoimmune encephalomyelitis (EAE).
In the present study, we conducted an intensive computational docking analysis to identify novel E-FABP inhibitors for regulation of immune cell functions and for treatment of EAE.
We demonstrate that compound [2-(4-acetylphenoxy)-9,10-dimethoxy-6,7-dihydropyrimido[6,1-a]isoquinolin-4-one; designated as EI-03] bound to the lipid binding pocket of E-FABP and enhanced the expression of peroxisome proliferator-activating receptor (PPAR) γ. Further in vitro experiments showed that EI-03 regulated DC functions by inhibition of TNFα production while promoting IL-10 secretion. Moreover, EI-03 treatment counterregulated T cell balance by decreasing effector T cell differentiation (e.g. Th17, Th1) while increasing regulatory T cell development. Most importantly, mice treated with this newly identified compound exhibited reduced clinical symptoms of EAE in mouse models.
Taken together, we have identified a new compound which displays a potential therapeutic benefit for treatment of MS by targeting E-FABP.
PMCID: PMC4427938  PMID: 25962726
Fatty acid binding protein; Antigen present cells; T lymphocytes; EAE
22.  Design of an Embedded CMOS Temperature Sensor for Passive RFID Tag Chips 
Sensors (Basel, Switzerland)  2015;15(5):11442-11453.
This paper presents an ultra-low embedded power temperature sensor for passive RFID tags. The temperature sensor converts the temperature variation to a PTAT current, which is then transformed into a temperature-controlled frequency. A phase locked loop (PLL)-based sensor interface is employed to directly convert this temperature-controlled frequency into a corresponding digital output without an external reference clock. The fabricated sensor occupies an area of 0.021 mm2 using the TSMC 0.18 1P6M mixed-signal CMOS process. Measurement results of the embedded sensor within the tag system shows a 92 nW power dissipation under 1.0 V supply voltage at room temperature, with a sensing resolution of 0.15 °C/LSB and a sensing accuracy of −0.7/0.6 °C from −30 °C to 70 °C after 1-point calibration at 30 °C.
PMCID: PMC4481890  PMID: 25993518
temperature sensor; RFID tag; CMOS process; phase-locked loop
23.  Balancing acts of SRI and an auto-inhibitory domain specify Set2 function at transcribed chromatin 
Nucleic Acids Research  2015;43(10):4881-4892.
Set2-mediated H3K36 methylation ubiquitously functions in coding regions in all eukaryotes. It has been linked to the regulation of acetylation states, histone exchange, alternative splicing, DNA repair and recombination. Set2 is recruited to transcribed chromatin through its SRI domain's direct association with phosphorylated Pol II. However, regulatory mechanisms for histone modifying enzymes like Set2 that travel with elongating Pol II remain largely unknown beyond their initial recruitment events. Here, by fusing Set2 to RNA Pol II, we found that the SRI domain can also recognize linker DNA of chromatin, thereby controlling Set2 substrate specificity. We also discovered that an auto-inhibitory domain (AID) of Set2 primarily restricts Set2 activity to transcribed chromatin and fine-tunes several functions of SRI. Finally, we demonstrated that AID mutations caused hyperactive Set2 in vivo and displayed a synthetic interaction with the histone chaperone FACT. Our data suggest that Set2 is intrinsically regulated through multiple mechanisms and emphasize the importance of a precise temporal control of H3K36 methylation during the dynamic transcription elongation process.
PMCID: PMC4446442  PMID: 25925577
24.  Surgical procedure determination based on tumor-node-metastasis staging of gallbladder cancer 
AIM: To investigate the impact of surgical procedures on prognosis of gallbladder cancer patients classified with the latest tumor-node-metastasis (TNM) staging system.
METHODS: A retrospective study was performed by reviewing 152 patients with primary gallbladder carcinoma treated at Peking Union Medical College Hospital from January 2003 to June 2013. Postsurgical follow-up was performed by telephone and outpatient visits. Clinical records were reviewed and patients were grouped based on the new edition of TNM staging system (AJCC, seventh edition, 2010). Prognoses were analyzed and compared based on surgical operations including simple cholecystectomy, radical cholecystectomy (or extended radical cholecystectomy), and palliative surgery. Simple cholecystectomy is, by definition, resection of the gallbladder fossa. Radical cholecystectomy involves a wedge resection of the gallbladder fossa with 2 cm non-neoplastic liver tissue; resection of a suprapancreatic segment of the extrahepatic bile duct and extended portal lymph node dissection may also be considered based on the patient’s circumstance. Palliative surgery refers to cholecystectomy with biliary drainage. Data analysis was performed with SPSS 19.0 software. Kaplan-Meier survival analysis and Logrank test were used for survival rate comparison. P < 0.05 was considered statistically significant.
RESULTS: Patients were grouped based on the new 7th edition of TNM staging system, including 8 cases of stage 0, 10 cases of stage I, 25 cases of stage II, 21 cases of stage IIIA, 21 cases of stage IIIB, 24 cases of stage IVA, 43 cases of stage IVB. Simple cholecystectomy was performed on 28 cases, radical cholecystectomy or expanded gallbladder radical resection on 57 cases, and palliative resection on 28 cases. Thirty-nine cases were not operated. Patients with stages 0 and I disease demonstrated no statistical significant difference in survival time between those receiving radical cholecystectomy and simple cholecystectomy (P = 0.826). The prognosis of stage II patients with radical cholecystectomy was better than that of simple cholecystectomy. For stage III patients, radical cholecystectomy was significantly superior to other surgical options (P < 0.05). For stage IVA patients, radical cholecystectomy was not better than palliative resection and non-surgical treatment. For stage IVB, patients who underwent palliative resection significantly outlived those with non-surgical treatment (P < 0.01)
CONCLUSION: For stages 0 and I patients, simple cholecystectomy is the optimal surgical procedure, while radical cholecystectomy should be actively operated for stages II and III patients.
PMCID: PMC4402309  PMID: 25914471
Gallbladder cancer; Simple cholecystectomy; Tumor-node-metastasis staging; Radical cholecystectomy; Prognosis
25.  Ocular surface changes in type II diabetic patients with proliferative diabetic retinopathy 
To detect and analyze the changes on ocular surface and tear function in type II diabetic patients with proliferative diabetic retinopathy (PDR), an advanced stage of diabetic retinopathy (DR), using conventional ophthalmic tests and the high-resolution laser scanning confocal microscopy.
Fifty-eight patients with type II diabetes were selected. Based on the diagnostic criteria and stage classification of DR, the patients were divided into the non-DR (NDR) group and the PDR group. Thirty-six patients with cataract but no other ocular and systemic disease were included as non-diabetic controls. All the patients were subjected to the conventional clinical tests of corneal sensitivity, Schirmer I Test, and corneal fluorescein staining. The non-invasive tear film break-up time (NIBUT) and tear interferometry were conducted by a Tearscope Plus. The morphology of corneal epithelia and nerve fibers was examined using the high-resolution confocal microscopy.
The NDR group exhibited significantly declined corneal sensitivity and Schirmer I test value, as compared to the non-diabetic controls (P< 0.001). The PDR group showed significantly reduced corneal sensitivity, Schirmer I test value, and NIBUT in comparison to the non-diabetic controls (P < 0.001). Corneal fluorescein staining revealed the progressively injured corneal epithelia in the PDR patients. Moreover, significant decrease in the corneal epithelial density and morphological abnormalities in the corneal epithelia and nerve fibers were also observed in the PDR patients.
Ocular surface changes, including blunted corneal sensitivity, reduced tear secretion, tear film dysfunction, progressive loss of corneal epithelia and degeneration of nerve fibers, are common in type II diabetic patients, particularly in the diabetic patients with PDR. The corneal sensitivity, fluorescein staining scores, and the density of corneal epithelial cells and nerve fibers in the diabetic patients correlate with the duration of diabetes. Therefore, ocular surface of the patients with PDR should be examined regularly by conventional approaches and confocal microscopy to facilitate early diagnosis and treatment of keratopathy.
PMCID: PMC4413579  PMID: 25938056
type II diabetes; proliferative diabetic retinopathy; ocular surface; corneal sensitivity; confocal microscopy; tear film break-up time

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